[backport] CI fixes (#6933)

* Relax shotgun test. (#6900)

It's non-deterministic algorithm, the test is flaky.

* Disable pylint error. (#6911)

* [CI] Skip external memory gtest on osx. (#6901)

* [CI] Fix custom metric test with empty dataset. (#6917)

* Reduce Travis environment setup time. (#6912)

* Remove unused r from travis.
* Don't update homebrew.
* Don't install indirect/unused dependencies like libgit2, wget, openssl.
* Move graphviz installation to conda.

* Relax shotgun test. (#6918)

* Relax test for decision stump in distributed environment. (#6919)

* Backport cupy fix.

.github/workflows/main.yml

@@ -31,7 +31,10 @@ jobs:
     - name: Run gtest binary
       run: |
         cd build
-        ctest --exclude-regex AllTestsInDMLCUnitTests --extra-verbose
+        # libomp internal error:
+        #   OMP: Error #131: Thread identifier invalid.
+        ./testxgboost  --gtest_filter="-HistIndexCreationWithExternalMemory.Test"
+        ctest -R TestXGBoostCLI --extra-verbose
 
   gtest-cpu-nonomp:
     name: Test Google C++ unittest (CPU Non-OMP)

.travis.yml

@@ -19,18 +19,10 @@ jobs:
       env: TASK=java_test
 
 # dependent brew packages
+# the dependencies from homebrew is installed manually from setup script due to outdated image from travis.
 addons:
   homebrew:
-    packages:
+    update: false
-      - cmake
-      - libomp
-      - graphviz
-      - openssl
-      - libgit2
-      - lz4
-      - wget
-      - r
-    update: true
   apt:
     packages:
       - snapd

python-package/xgboost/core.py

@@ -1872,7 +1872,9 @@ class Booster(object):
                 )
             )
             return _prediction_output(shape, dims, preds, False)
-        if lazy_isinstance(data, "cupy.core.core", "ndarray"):
+        if lazy_isinstance(data, "cupy.core.core", "ndarray") or lazy_isinstance(
+            data, "cupy._core.core", "ndarray"
+        ):
             from .data import _transform_cupy_array
             data = _transform_cupy_array(data)
             interface = data.__cuda_array_interface__
@@ -2027,7 +2029,7 @@ class Booster(object):
         """
         if isinstance(fout, (STRING_TYPES, os.PathLike)):
             fout = os.fspath(os.path.expanduser(fout))
-            fout = open(fout, 'w')
+            fout = open(fout, 'w')  # pylint: disable=consider-using-with
             need_close = True
         else:
             need_close = False

tests/ci_build/conda_env/macos_cpu_test.yml

@@ -15,6 +15,7 @@ dependencies:
 - matplotlib
 - dask
 - distributed
+- graphviz
 - python-graphviz
 - hypothesis
 - astroid

tests/python/test_linear.py

@@ -57,15 +57,13 @@ class TestLinear:
         param['updater'] = 'shotgun'
         param = dataset.set_params(param)
         result = train_result(param, dataset.get_dmat(), num_rounds)['train'][dataset.metric]
-        # shotgun is non-deterministic, so we relax the test by sampling
+        # shotgun is non-deterministic, so we relax the test by only using first and last
-        # result.
+        # iteration.
         if len(result) > 2:
-            sampled_result = [score for i, score in enumerate(result)
+            sampled_result = (result[0], result[-1])
-                              if i % 2 == 0]
-            sampled_result[-1] = result[-1]  # make sure the last one is used
         else:
             sampled_result = result
-        assert tm.non_increasing(sampled_result, 1e-3)
+        assert tm.non_increasing(sampled_result)
 
     @given(parameter_strategy, strategies.integers(10, 50),
            tm.dataset_strategy, strategies.floats(1e-5, 2.0),

tests/python/test_with_dask.py

@@ -1023,7 +1023,17 @@ class TestWithDask:
                                  evals=[(m, 'train')])['history']
         note(history)
         history = history['train'][dataset.metric]
-        assert tm.non_increasing(history)
+
+        def is_stump():
+            return params["max_depth"] == 1 or params["max_leaves"] == 1
+
+        def minimum_bin():
+            return "max_bin" in params and params["max_bin"] == 2
+
+        if minimum_bin() and is_stump():
+            assert tm.non_increasing(history, tolerance=1e-3)
+        else:
+            assert tm.non_increasing(history)
         # Make sure that it's decreasing
         assert history[-1] < history[0]
 

tests/python/testing.py

@@ -272,6 +272,8 @@ def eval_error_metric(predt, dtrain: xgb.DMatrix):
     label = dtrain.get_label()
     r = np.zeros(predt.shape)
     gt = predt > 0.5
+    if predt.size == 0:
+        return "CustomErr", 0
     r[gt] = 1 - label[gt]
     le = predt <= 0.5
     r[le] = label[le]

tests/travis/run_test.sh

@@ -1,7 +1,5 @@
 #!/bin/bash
 
-make -f dmlc-core/scripts/packages.mk lz4
-
 source $HOME/miniconda/bin/activate
 
 if [ ${TASK} == "python_sdist_test" ]; then

tests/travis/setup.sh

@@ -1,5 +1,9 @@
 #!/bin/bash
 
+# https://travis-ci.community/t/macos-build-fails-because-of-homebrew-bundle-unknown-command/7296/27
+brew install cmake libomp lz4
+
+
 if [ ${TASK} == "python_test" ] || [ ${TASK} == "python_sdist_test" ]; then
     if [ ${TRAVIS_OS_NAME} == "osx" ]; then
         wget --no-verbose -O conda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh